**From:** Ashutosh Shandilya (*scfbioiitd_at_gmail.com*)

**Date:** Wed Nov 17 2021 - 13:08:38 CST

**Next message:**Giacomo Fiorin: "Re: colvars: Too many iterations in routine jacobi."**Previous message:**Giacomo Fiorin: "Re: colvars: Too many iterations in routine jacobi."**In reply to:**Giacomo Fiorin: "Re: colvars: Too many iterations in routine jacobi."**Next in thread:**Giacomo Fiorin: "Re: colvars: Too many iterations in routine jacobi."**Reply:**Giacomo Fiorin: "Re: colvars: Too many iterations in routine jacobi."**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

I increased harmonic restrain to 5.0 using command

abf {

colvars gs

fullSamples 1000

historyfreq 100000

hidejacobian off

}

harmonic {

colvars gs

centers 0.0

forceconstant 5.0

}

Output file shows the same RMSD for all the structures something like this

which should not be the case. Is it because i switched off

*usesecondclosestframe* off. I have been trying to change several

parameters in the input but still getting some kind of error.

Frame index: 67 ; optimal RMSD = 0.985712

Frame index: 80 ; optimal RMSD = 0.985712

Frame index: 79 ; optimal RMSD = 0.985712

Frame index: 78 ; optimal RMSD = 0.985712

Frame index: 77 ; optimal RMSD = 0.985712

Frame index: 76 ; optimal RMSD = 0.985712

Frame index: 75 ; optimal RMSD = 0.985712

Frame index: 74 ; optimal RMSD = 0.985712

Frame index: 73 ; optimal RMSD = 0.985712

Frame index: 72 ; optimal RMSD = 0.985712

Frame index: 71 ; optimal RMSD = 0.985712

Frame index: 70 ; optimal RMSD = 0.985712

Frame index: 69 ; optimal RMSD = 0.985712

Frame index: 68 ; optimal RMSD = 0.985712

Frame index: 81 ; optimal RMSD = 0.985712

Frame index: 66 ; optimal RMSD = 0.985712

Frame index: 65 ; optimal RMSD = 0.985712

Frame index: 64 ; optimal RMSD = 0.985712

Frame index: 63 ; optimal RMSD = 0.985712

Frame index: 62 ; optimal RMSD = 0.985712

Frame index: 61 ; optimal RMSD = 0.985712

Frame index: 60 ; optimal RMSD = 0.985712

Frame index: 59 ; optimal RMSD = 0.985712

Frame index: 58 ; optimal RMSD = 0.985712

Frame index: 57 ; optimal RMSD = 0.985712

Frame index: 56 ; optimal RMSD = 0.985712

Frame index: 55 ; optimal RMSD = 0.985712

Frame index: 94 ; optimal RMSD = 0.985712

Frame index: 107 ; optimal RMSD = 0.985712

108 PDB structures were obtained from the PNEB path. I computed RMSD with

VMD which is mentioned below. Kindly have a look and suggest. My actual

RMSD varies like this.

1 0.5520958304405212

2 0.6408998370170593

3 0.7004873752593994

4 0.7478375434875488

5 0.7849769592285156

6 0.8124300241470337

7 0.829501748085022

8 0.8617943525314331

9 0.8889437317848206

10 0.9140389561653137

11 0.925011396408081

12 0.931750476360321

13 0.9490005373954773

14 0.9639561176300049

15 0.9865623712539673

16 1.0129530429840088

17 1.017659068107605

18 1.0304405689239502

19 1.05254328250885

20 1.0523943901062012

21 1.0497472286224365

22 1.0674532651901245

23 1.0869779586791992

24 1.1080254316329956

25 1.1066851615905762

26 1.1148474216461182

27 1.1117987632751465

28 1.1251643896102905

29 1.1315655708312988

30 1.1351579427719116

31 1.1500359773635864

32 1.1598128080368042

33 1.1690787076950073

34 1.1832456588745117

35 1.190578579902649

36 1.1949034929275513

37 1.2126442193984985

38 1.2073010206222534

39 1.2080799341201782

40 1.2127560377120972

41 1.2220537662506104

42 1.2297075986862183

43 1.2463030815124512

44 1.258796215057373

45 1.2574396133422852

46 1.2649439573287964

Kindly suggest.

Thanks,

Ashutosh

On Wed, Nov 17, 2021 at 1:32 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>

wrote:

*> There *were* multiple RMSD computations, because that's how the distances
*

*> between path frames are computed.
*

*>
*

*> You are also omitting several warnings above, btw. One was "Please check
*

*> your configuration or increase restraint on z(σ)". What did you do there?
*

*>
*

*> I don't know where you got the PDB structures from, but I recommend that
*

*> you load them in VMD and compute the RMSD of the coordinates of your
*

*> simulation with respect to each. All RMSDs need to be well defined in
*

*> order to be able to compute the path variable derived from them.
*

*>
*

*> Giacomo
*

*>
*

*>
*

*> On Wed, Nov 17, 2021 at 12:55 PM Ashutosh Shandilya <scfbioiitd_at_gmail.com>
*

*> wrote:
*

*>
*

*>> Thanks for your reply, As I understand I should consider the selection
*

*>> which has only moderate change. First step itself gives this problem so I
*

*>> have not calculated the RMSD. I have a string of pdbs from PNEB path and I
*

*>> want to have a pmf that's why I am using abf. So the selected atoms have
*

*>> lots of transformation. So what are the options.
*

*>>
*

*>> Many thanks,
*

*>> Ashutosh
*

*>>
*

*>> On Wed, Nov 17, 2021 at 11:28 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
*

*>> wrote:
*

*>>
*

*>>> This message is the key:
*

*>>> colvars: This is usually the result of an ill-defined set of atoms for
*

*>>> rotational alignment (RMSD, rotateReference, etc).
*

*>>>
*

*>>> If the structure of the group of atoms changes too much, it becomes
*

*>>> possible that a pure rotation is not the transformation that minimizes the
*

*>>> RMSD, but another transformation does (e.g. rotation + reflection across a
*

*>>> plane).
*

*>>>
*

*>>> You do not need to change the time step, but instead pick a selection
*

*>>> that is guaranteed to have only moderate changes in structure. Practically
*

*>>> speaking, the RMSD should remain much lower than the radius of gyration--000000000000aa525805d100d26a--
*

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